Network-based drug repositioning
Network-based computational biology, with the emphasis on biomolecular interactions and omics-data integration, has had success in drug development and created new directions such as drug repositioning and drug combination. Drug repositioning, i.e., revealing a drug's new roles, is increasingly attracting much attention from the pharmaceutical community to tackle the problems of high failure rate and long-term development in drug discovery. While drug combination or drug cocktails, i.e., combining multiple drugs against diseases, mainly aims to alleviate the problems of the recurrent emergence of drug resistance and also reveal their synergistic effects. In this paper, we unify the two topics to reveal new roles of drug interactions from a network perspective by treating drug combination as another form of drug repositioning. In particular, first, we emphasize that rationally repositioning drugs in the large scale is driven by the accumulation of various high-throughput genome-wide data. These data can be utilized to capture the interplay among targets and biological molecules, uncover the resulting network structures, and further bridge molecular profiles and phenotypes. This motivates many network-based computational methods on these topics. Second, we organize these existing methods into two categories, i.e., single drug repositioning and drug combination, and further depict their main features by three data sources. Finally, we discuss the merits and shortcomings of these methods and pinpoint some future topics in this promising field.